Xiuwen Zheng
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/SNPRelate |
| git_branch: RELEASE_3_20 |
| git_last_commit: 80684f3 |
| git_last_commit_date: 2024-10-29 09:54:31 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2000/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SNPRelate 1.40.0 (landing page) Xiuwen Zheng
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the SNPRelate package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNPRelate.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SNPRelate |
| Version: 1.40.0 |
| Command: rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SNPRelate.buildbin-libdir |
| StartedAt: 2024-11-20 04:52:46 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 04:53:29 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 42.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SNPRelate_1.40.0.tgz |
| PackageFileSize: 3.826 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SNPRelate.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SNPRelate.buildbin-libdir SNPRelate_1.40.0.tar.gz' >>>>>>> * installing *source* package ‘SNPRelate’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_SNPRelate.c -o R_SNPRelate.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SNPRelate.cpp -o SNPRelate.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ThreadPool.cpp -o ThreadPool.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dGenGWAS.cpp -o dGenGWAS.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dVect.cpp -o dVect.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genBeta.cpp -o genBeta.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genEIGMIX.cpp -o genEIGMIX.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genFst.cpp -o genFst.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genHWE.cpp -o genHWE.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genIBD.cpp -o genIBD.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genIBS.cpp -o genIBS.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genKING.cpp -o genKING.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genLD.cpp -o genLD.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genPCA.cpp -o genPCA.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genSlideWin.cpp -o genSlideWin.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -lpthread -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/SNPRelate.buildbin-libdir/00LOCK-SNPRelate/00new/SNPRelate/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SNPRelate) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so >>>>>>> >>>>>>> Paths before fix: SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so: SNPRelate.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so" >>>>>>> Paths after fix: SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so: SNPRelate.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)